In December, 1995, the Institute of History and Philology of Academia Sinica started the archaeological investigation of Tainan Science Park. And Tree Valley Foundations Archaeology Center continued investigation and excavation of Tainan Science Park Special Zone. To date, there are 82 archaeological sites in Tainan Science Park and neighboring area. Among them there are 28 sites in Tainan Science Park, 14 sites are in Tree Valley Park, and the remaining 40 sites are distributed across the Tainan Science Park Special Zone and neighboring area.These sites date back to the prehistoric time period of Taiwan, covering a time span of 300 to 5,000 years B.P. It has been chronologically divided into six phases: Tapenkeng Culture, Niuchoutzu Culture, Tahu Culture, NiaoSung Culture, Siraya Culture and recent Han-Chinese Culture. In order to keep these priceless treasures, the project of setting up a museum inside Tainan Science Park has been undertaken by the National Museum of Prehistroy.

Through the artificial relics and ecological remains collected, the general concepts of museum exhibitions including the following four fields:

1. To explain what archaeology is and how it works. Introducing the significance of the discoveries at Tainan Science Park.
2. To demonstrate the ecological environment and transition in southern Taiwan.
3. To reconstruct the human lifestyle and cultural changes in each era, and also to display the continuing progress of human activities on this land.
4. To present the development of modern technology industry and the concept of sustainable management at Tainan Science Park.